A Certain Second Magic
by PML7
Summary: Rin Tohsaka has always been an excellent student, to the point of impressing her current mentor, Zelretch himself. The time for book learning is over for her. Time to put her knowledge to use during field training. Too bad Zelretch's version of field training is bit more expansive than most magi…. (Takes place during the SIster's Arc.)
1. Chapter 1

A Certain Second Magic

-Disclaimer- Fate/Stay Night is owned by Type Moon. The Indexverse was created by Kazuma Kamachi and published by ASCII Media Works. This work will be based mostly on FSN Heaven's Feel, Fate Zero, and A Certain Scientific Railgun. No infringement is intended.

Summary- Rin Tohsaka has always been an excellent student, to the point of impressing her current mentor, Zelretch himself. The time for book learning is over for her. Time to put her knowledge to use during field training. Too bad Zelretch's version of field training is bit more expansive than most magi….

**Story start**

Rin stared at her pendant. It was cross shaped to show her heritage, if not her true religious persuasion. For Rin Tohsaka was a Magus first and always. Her family did have unusually good ties with the Church, and Rin saw no need for that to change.

Besides it would let her wear the pendant at all times. Who would suspect the religious icon of being a magical foci?

For that is what she had made.

Three years of working here in the Clocktower. Of the clamoring apprentices that had jumped at the call of learning from the revered and feared Wizard Marshall Zelretch himself, only she and Luvia remained. They were no longer truly enemies, certainly not after a series of misadventures that all of the apprentices had faced.

That didn't make them friends. Luvia had completed her bracelet three days ago, beating Rin at the challenge. A movable point that was always connected to her room in the Clocktower, that would allow her to tap into one of the greatest flows of mana from around the world, even if the local area was dry.

Rin sighed and remembered the heady feeling of wielding a copy of the Jeweled Sword itself. Infinite power from infinite worlds. She looked at her pendant, such a small start.

But it was all hers.

Zelretch entered, "So my dear. Have you finally caught up to your rival?"

"Yes Master." Rin handed the pendant to Zelretch.

He examined it and nodded. "Good work. You and Luvia are farther along the path than I think either of you realize." He smiled. It wasn't a pleasant smile. It was an evil smile that usually preceded some sort of practical joke. "You are ready for field training. Which is good, I sent Luvia to her designated mission target this morning. You don't want to fall too far behind the girl, hmm?"

Rin shook her head. What was she in for? "Do I have time to pack? I mean it is winter and I am dressed for inside and…."

Zelretch patted her on the back, "No need. It is summer where you are going. And I will provide enough for you to assemble a reasonable wardrobe for your period in Academy City."

Rin looked up at him, trying to master her fears, "What about the language? Surely I need at least a little time for that?" She had worked on a translation spell, but it was still slow and awkward. It was amazing how broad a spectrum of spells you learned if you feared that tomorrow you might end up anywhere or anywhen.

"Oh, come now Rin. You faced off against the entire Clocktower. You survived Heaven's Feel. You faced and defeated Angra Mainyu. Surely such a small trip won't kill you!"

"Can I at least scrounge up some notes?"

Zelretch shook his head, "Flexibility and adaptability are one of the fundamental concepts if one is going to utilize the Second Magic." He sighed, "Really Rin, I assumed you would be at least a little more accepting that the Luvia girl. She had a privileged background, so I expected some whining. But you, I had high hopes you would simply show me the spark I saw the first day we met, that you would be ready to accept your fate and go down swinging."

Rin took a deep breath. There was no point fighting this. She quickly grabbed what she had around her and let her face achieve her typical mask. "Very well. Let's go."

The world twisted and they were on a balcony overlooking a city surrounded by a wall. Inside were numerous windmills and buildings. She saw a series of airships floating by, the weather broadcast on a massive marquee. The language of the surrounding signs was a mix of Japanese and English.

She felt a slight wash of hope wash into her. It wasn't some far distant world. Things were different, like those airships, but not too different.

Zelretch scanned the City, "This is Academy City. This world's premier city of science. Hah."

Rin looked around again. Lots of electronics. A different sinking feeling. She wasn't a technophobe like many of the Magi she knew, but she had only learned the basics back home while in High School. "What do you need me to do here?"

Zelretch didn't look at her, just scanned the horizon. "2.3 million People, most of them kids. All learning how to become psychic. With Science."

"Sir?"

"My contact will fill you with most of the details about this place. It will probably take a day or two to get your paperwork settled in the first place. But I have sensed something dark going on here. Something beyond this world, and possibly from ours or a world close to ours." He looked over at her, "The Magic signature is similar to ours. Oh, that reminds me. Magic works here. Mana is pretty easy to come by. But I would stick to the mana you get out of your pendant. That will be drawn from our world and will be limited by its constraints. Our conceptual magic will not work normally here. This world's magic is based on faith and religion. Emiya will tell you more."

"E,emiya?"

"Kiritsugu Emiya fled here with his daughter about seventeen years ago. Interesting if frightfully sad story, maybe he will tell you it. Maybe he won't. He doesn't have a deep love of Magi. I knew the moment he left his world and helped him out when he got here. We have been helping each other ever since. Useful man."

"Kiritsugu Emiya? As in…."

"His was a different world from ours." Zelretch paused, and for the first time she felt an emotion other than playfulness or boredom from him. He seemed sad, "I tried to save Iri. Not just for Kiritsugu, but for old Justeaze. It isn't really my place to get involved unless it seriously threatens the world order, even my power has limits." He forced a smile, "But that isn't important now. I need to go buy my God Daughter a bikini or two. A friend recommended Seventh Mist downtown. Tell, Ilya I said hi!" And he began walking off.

Rin stared at him for a moment. He was just going to leave her here? In the middle of a park? "But, Master!"

He turned around; walking backwards, "Don't worry. Someone should be here shortly to pick you up." He then kicked his heels and headed into what appeared to be a shopping district.

Rin frowned and then wiped her brow. Zelretch had been right about not needing a jacket. It was quite warm. She froze as a series of robots rushed past her muttering about property damage. Two middle school girls appeared out of nowhere, with one chastising the other about being more lady like.

Teleportation? They could teleport here? Her mind began to freeze at the possibilities. She unconsciously tried to cast a simple scanning spell. But her head began to spin as it failed.

He had abandoned her in a world where her magic didn't work? She was defenseless? And they could teleport?

She needed space, someplace to regain her calm and focus. But the botched spell was still causing her to be dizzy. Which likely explained what happened next.

"Hello. You seem lost. Are you by chance Rin Tohsaka?"

Rin just stared. The man was wearing a black uniform that covered most of his body. It looked similar though different to Archer's armor. It did lack the red shroud Archer had always been so proud of. He was tall, as tall as Archer, and with a similar build. But his hair and eyes were even more familiar.

She couldn't believe it, "Shirou? Shirou Emiya?" The world continued to spin. She felt familiar arms support her. How often in her dreams had he held her?

How many times had she wished for this? Secretly cursing her sister's luck, even as she was so very grateful for Sakura's salvation?

Shirou said something to her.

She only smiled up at him. Was he Archer? Or was he Emiya? Did it matter in the end? They were after all the same person. A person she trusted like she trusted few others.

A person in whose arms she was safe. Safe to let the world pass her by for a moment while her mind recovered.

He patted her cheek and looked closely at her eyes. He said something, but she didn't care. His eyes were beautiful. She cared more about that.

She was safe.

She was tired.

And so she slept.

**End Part**

A/N- Sigh. So little time. So many ideas. This was a plot bunny that refused to die. An Opportunity of Fate takes precedence on this story, if only because this one is shorter. But maybe an extra story will prompt me to actually write and not stare at the screen while listening to music. Let's hope.

As for timing, this story takes place during Sister's Arc for both Index and Railgun. Rin is from a world where the Heaven's Feel true occurred. So she is working with Zelretch and by stories start has for several years. Kiritsugu, Ilya, and Shirou are from differing but similar timelines. All part of the story.

Hope you enjoy.


	2. Chapter 2

A Certain Second Magic part 2

Shirou stared down at the beautiful woman he was holding. Was she the Rin Tohsaka he had been ordered to find? Dad had been shy on details, just it was one of the 'Old Man's' protégés who would be dropped off in the park in District 7.

Shirou shivered. That old man frightened him. Sure he and dad were good friends, and he loved Ilya. There was something not right about him. It wasn't that he was alien from this world. His whole family was. It wasn't that he wasn't fully human either. Ilya was a hybrid of some sort too; it was why she'd needed all that time in the hospital.

There were times when Shirou wished he could go back to the real world and wipe Einzbern Castle off the map. How could someone do that to a little girl? Not just the physical differences, but the deliberate alterations that would have kept Ilya prepubescent through her unnaturally short and painful life. She had been cured of most of it, but even now she visited the hospital once a month to make sure there were no residual effects.

Shirou shook his head. No, the real reason Old Man Zelretch frightened Shirou was because he was neither living nor dead. How someone could be both escaped Shirou, only he could sense a slowly creeping corrosion affecting the old man both in body and soul. And if this girl was his protégé, did she suffer the same ailment?

Many were the simple days when he wished he were simply an Esper like Ilya. To be able to connect to the ambient mana that filled this world must be great. To be able to then focus it on whatever your special talent was…. It must be easier than this.

There was a hidden switch inside of his head, and when he threw it, power would course through his body. And with it pain. He would then filter the prana for the od his magic needed. He took a deep breath.

"Trace on!"

The whole process took less than a second, and he could feel the warmth of his circuits heat his body. He felt as the suit began to adjust its cooling properties to maintain optimum temperature. This was his personal suit after all; the first step in his dream of making a working mecha that could be used to save people.

A brief dream of Shirou standing against the forces of darkness in a giant robot, finishing them off with a giant blazing sword and….

Not going to happen. Any more than his childish dreams of swords; the day of swords as a primary combat weapon were long gone. Even with power armor, you yielded much more effectiveness using firearms or energy weapons. The most he could hope for were some of those machines he had seen MAR working with.

Shirou did most of his work for Anti-Skill and the Security bots they depended on. They did have some specialist equipment that was difficult to work on, and Shirou had learned much how they worked in his repairs.

He looked down at the girl. "_**Structural Analysis**_"

Streams of data began to flow into his mind. The basics of her construction flooded into him.

She was indeed a human. A magus just like himself, and she had swept unfiltered prana into her circuits. Uncomfortable and disorienting. But she would recover.

Shirou moved a lock of hair from her face. "Well, you can't talk to me yet, but I am guessing you are Rin Tohsaka after all." He lifted her up. "Let's get you home. Dad is waiting."

The next part was harder. Kiritsugu Emiya was a very poor teacher as a magus, although his self-defense courses he taught at a variety of Academies were highly sought after. While he had taught him enough not to kill himself activating his circuits, most of what he knew was pointless in Academic City, depending on mysteries that this world had not been imprinted in. Only internal magic worked even close to normal. Kiritsugu had taught both himself and Ilya basic self-healing spells and basic reinforcement. But that was it. And unlike Ilya, Shirou didn't have Esper powers.

All Shirou had in a school were superpowers were common were a few magic tricks. To do anything more required a pattern on which his powers and the world could relate to. And to his horror he had found a way.

Math. Lots and lots of math. It was how Espers controlled their powers. When Ilya had started bringing home the harder calculus books and explained what she used them for in running calculations for her Thermal Point power, Shirou knew he had found the solution.

He cleared his mind and began running the basic calculations that would allow him to reinforce both himself and his suit. That should allow him to carry sleeping beauty all the way home.

Plus it was fun. Anyone who saw him would think it was either the actuators of his suit or some odd Esper power.

Shirou smiled. He just wished he hadn't left his helmet at home.

Well his father would yell at him later. Now was time for a little stretching of his legs. "_**Reinforce**_"

Shirou rigged a working safety harness for Rin, and once he was certain he wouldn't lose her, he began to run. Within fifty meters he was running faster than humanly possible (without assistance). As his speed climbed up to more than fifty kilometers per hour, he reluctantly altered some of the parameters of the spell and kept it to maintain his current pace.

He was doing enough damage to the park as it was. Of course he was almost out of it, so that would help. Of course there was the road of course. And at this time of day it was busy.

Sigh.

All it took was a few quick calculations, a slight twist of direction, up three stairs and using the stair balcony to propel him up and over the street and its annoying traffic. He lost a little speed with that trick, and he knew he needed to lose more.

He heard his cargo muttering something about Archer and bumpy rides. But somehow she remained asleep. It did remind him that he had more than his own enjoyment to pay attention to.

The park had been relatively open; these sidewalks were not safe to move at high speeds on. The last thing Shirou needed to explain was why he ran over a bunch of elementary kids.

Well he wasn't far from home. Slowing down would be okay. He kept the spells working as might come in handy.

Or he might be able to cut across a relatively empty lot nearby and really play out his speed. He got to use the strength and durability enhancements often, speed much less so. Really what other city could you do this in?

He was getting a few looks for carrying a woman. But typically they saw the Anti-Skill logo and they left him alone. Sure, none of the captains ever took him out to the field, sure he ended up fixing way too much broken equipment, but there were still perks to volunteering to work with Anti-Skill.

"Touma! Catch him, Sphinx will get squashed by a car if she makes it to the road!"

Shirou was grateful for keeping his spells up, as they also increased his agility. Necessary as teenager came barreling around the corner chasing a cat. Shirou watched the poor teens eyes widen.

"Such misfortune!" said the teen.

Shirou managed to keep himself from being entangled with the poor teen, but was also unable to break the kid's fall. And he landed hard.

A short haired nun came after the teen. "Touma! What are you doing lying on the ground? Sphinx is still in danger." She turned to face Shirou, "Can you help us?" She then saw Rin, "Or maybe we should be helping you."

Shirou shook his head, "She will be fine. I am just taking her home. As for the cat…." He turned and saw the cat, "Well that is more a call for Judgment, but since I am here." Shirou watched as the cat crawled up a trellis and onto a ledge.

Meow.

The nun was pounding on the teen to get up and fetch the cat.

In that kid's stunned condition, he would most likely end up hurting himself.

Options.

If he were not carrying Rin, he could climb up himself. Of course the trellis wouldn't support his weight, even if he dropped off Rin. That would mean his climbing tools. And an expensive repair bill.

Next option?

Walk away. It wasn't his problem. He could even contact Judgment for them. Surely one of the Espers in the area would be an expert at fetching cats.

Except that would look bad and reflect poorly on Anti-Skill. If it got back to one of the captains he would never hear the end of it. He knew he had a reputation for recklessness, but only with himself. He was always careful that no one else got hurt. If he did, what did it matter?

In this world you couldn't protect everyone, but Shirou would certainly try.

Okay. This was simply another problem. He had to figure out what he had on his suit or in the environment that would allow him to get the cat. None of the gear he had on himself would be fatal. If used on a human.

Shirou wasn't sure what his subsonic rubber bullets would do to a cat, but it would probably not be wise. The electric shock didn't reach that far.

Well. There was the tranquilizer gun. He only had it because he was occasionally attacked when he was on a repair. The active ingredient was supposed to be safe in most mammals, and well a cat was a mammal. He lowered the dose all the way down. "Sorry, kitty, this might hurt a little."

He raised his arm to shoot the cat.

The nun looked up at him and yelled, "I wanted your help to capture, not kill him!" She looked down, "Touma, stop him or he will kill Sphinx!"

The teen got up and gave Shirou a stare he had seldom seen before. "Put down that gun."

Shirou looked at the teen, "Touma, huh? Well Touma, this gun is a tranquilizer. We shoot the cat and it tumbles down and we catch it. You go your way, I go mine, both of us happy, except maybe a slightly sick kitty. Trust me the tranquilizer is safe, I've been hit by it before."

"I don't trust him Touma. We are not shooting Sphinx!"

"Index, he works for Anti-Skill… Maybe he knows best…."

"Touma!"

"Such misfortune." Touma said as he rushed Shirou.

A Shirou Emiya who had been trained in hand to hand combat by Kiritsugu Emiya. A Shirou Emiya who had gotten into constant fights to stop the bullying he saw occurring around him. And a Shirou Emiya who was currently Reinforced to beyond human capabilities.

The fight was over in seconds. But they were interesting seconds. For when they were fighting, as Shirou was setting up poor Touma to slam into a wall, Touma's right hand brushed up against him.

Both felt a massive jolt as Imagine Breaker reacted to Shirou's magic. For just a split second felt as his Reinforcement began to fail, as the ambient mana was denied to it.

But Shirou's spells didn't run on mana. They ran on od. And while his circuits burned a little for a moment, unable to separate the two aspects of prana, the moment passed. His spells remained in force.

Weakened and damaged. But not dispelled.

Shirou took a couple of pictures of Index and Touma for his files. He would want to find out more about the teen. And the girl had the look of a religious fanatic, dressed so heavily in robes. He would have to tell Dad that a possible magic user was in the City.

But first he had to get Rin safely home. He had been wasting too much time.

The nun, Index was caring for the teen and glaring at Shirou.

Shirou pivoted and shot Sphinx. It wavered a moment and fell. Into Shirou's enhanced hands. He handed it to Index. "Good night."

At least one of the security cameras had to have caught this incident. Shirou spent the rest of the run home trying to think of a way to explain all of it to Papa Kiritsugu….

**-End Part-**

A/N- So now you know a little about Shirou. And note that Index magic and Nasu magic both have advantages and strengths. Do not assume that by the above part that Nasu magic is stronger, but it does have advantages. So does Index magic. They are simply different.

Hope you folks continue to enjoy.


	3. Chapter 3

A Certain Second Magic part 3

Mikoto Misaka, the Ace of Tokiwadi, the famed Railgun, sank deeply into her chair and wondered what she had done. The Head Mistress was reading a series of reports behind her desk, and she was flanked by not only her Dorm Mother, but also the one from the alternate dorm.

She knew her own all too well from the occasional fights she had with Kuroko. The other had as fearsome a reputation, preferring a different style of holds than her own Dorm Mother's casual neck snaps, but supposedly as scary. MIsaka glanced at her cautiously and noted that alternate had a similar style of dress to her Dorm Mother, but it was if anything more severe. And black, to the point of making the woman's skin seem pale.

Misaka's attention reverted to the Head Mistress as she cleared her throat.

The distinguished looking woman sighed, "MIkoto, what are we going to do with you?" She glared at Misaka, "The documents I have here are congratulatory and speak highly of your actions in retrieving some children that were being held by MAR. They are considering breaking up the organization. Although what we would do without them I am not sure. Certainly, if the information is correct that Lifeline woman needs to be put away. This is a civilized City."

Misaka just fidgeted slightly and wondered how this was going to impact her.

The Head Mistress continued, "A decent amount of property damage, all of which the City has claimed responsibility for, thank heavens." She sighed and set the documents down, "You and Kuroko have been given awards for your service to Academic City. I was also asked to relay the need to follow proper channels and protocol next time. And given your history I do fear there will be a next time. Kuroko at least is part of Judgment. That buffers her somewhat from some of the legal aspects of what you both were involved in. Are you sure you don't wish to join? I have no doubt they would be ecstatic for your participation, finally managing to convince one of the Level Five's to join…."

Misaka said quietly, "No ma'am. I will help where I can, but I have no interest in formally becoming a member of Judgment."

The other Dorm Mother smiled, "Why not ask her to join Anti-Skill while we are at it."

Her Dorm Mother glared at the other, "Mikoto is only thirteen! Judgment alone is…"

The other Dorm Mother merely smiled, "Oh, you might be surprised at what a well-trained thirteen year old can do.

The Head Mistress spoke, "Tanaka, Hisau, we have already discussed this." They both grew silent. She turned to face Mikoto, "The truth is, I, and the school as a whole, would prefer that you did not get involved in these situations. Violence is often the worst option available. We seek to build your characters as such that it would not be necessary." She glanced over at Hisau, "Even while we train you girls in self-defense so that you can be prepared for any eventuality. We hope that none of it required. That it merely provides discipline and exercise."

There was a long pause while the Head Mistress wiped her glasses. She put them back on and glared at Mikoto, "However, you keep getting involved in dangerous situations. So far you have done well, but it is our belief that you, much like your troublesome roommate, will continue this trend." She sighed there is an unspoken rule here at Tokiwadai, fighting is not encouraged. But if by some horrible circumstance violence is the only option, you must win. Even in a fight you are representing Tokiwadai, and while we are not in the habit of raising warriors here at our girl's school, we aim to present ourselves as competent in all circumstances. Do you understand me, Mikoto Misaka?"

Mikoto shrank back in her chair. She had never seen the Head Mistress so angry or worried. Had she done something wrong? "Yes, Ma'am. I will try to avoid…"

The Head Mistress raised a hand to pause her and said, "I have given thought to this Mikoto. Hisau, if you please."

"As the Head Mistress indicated, we want you girls prepared for anything. Since you have a nose for trouble, I have asked a friend of mine to add you to his clientele. It will be added to your program, and you will be graded for your work. Kiritsugu Emiya can be a difficult man to work with, but he is good at thinking outside of the box and providing the training you want and need." Hisau smiled fondly. "While the general outlook and training regimen will be added to your records, the specifics will not."

The Head Mistress sighed again, "This is for your benefit, even if most specialized training comes in High School or College; you apparently need this now. You will receive your updated schedule in the next few days. That is all. Try to stay out of trouble. Today at least. You may not know it but you are the face of this whole City not just Tokiwadai, make us proud."

Mikoto stood and turned to leave.

Her Dorm Mother called out. "Mikoto, remember my door is always open."

"Mine, too." Hisau said, "Remember that you are not alone. I have…."

Mikoto turned and for just a moment a flash of dark emotion swept across Hisau's face. Then it was gone.

She looked away, "Not important at the moment. But if your dreams bother you or you need help dealing with after action stress, I know of ways to cope."

Mikoto simply nodded. As she left, she heard a quiet conversation begin. Did she want to know what they were saying? Not that it mattered as the heavy door shut. She touched it lightly and sighed.

She was a troublemaker now? Just because she had done what was right instead of taking an easier route. "Oh, man." Saddled with an additional class where she would be pestered about her abilities. She rubbed her hand through her hair.

She needed to decompress. Shopping maybe. She should check with Kuroko, see if she wanted to come. She walked to her room.

Kuroko ignored her entrance and kept typing at the computer.

Must be something going on with Judgment.

She quietly grabbed her purse and prepared to leave.

"So that is how it is going to be. Just leave out poor Kuroko. Ignore her. Pretend she doesn't exist."

"Sorry. You looked busy. I didn't want to bother you."

Kuroko turned and glared at her, "Is that why you ignored me earlier today? Just ducking around the corner when I called your name"

"I don't remember doing that. I spent most of today in the Library any way. Had a run in with the Queen." Mikoto shook her head.

Kuroko winced. "How did it go?"

Mikoto looked down," About as well as expected. I told her to leave you and my friends alone. She threatened me with everyone in the Library. She possessed everyone! All at once!"

Kuroko blinked over and gave a gentle tap to Mikoto's head. "She can't get in your head. That frightens her."

Mikoto brushed Kuroko off her head. Any touch could lead to clinging. You had to be careful with Kuroko. "Doesn't she frighten you?"

Kuroko looked away, "For someone to be able to so casually take over my mind…. Yes, she frightens me. All high power Espers are dangerous, the Level Fives simply take it to a new level. Yes the Queen scares me."

Mikoto felt her heart drop, "Are you afraid of me?"

Kuroko looked at her sincerely, "By all rights I should. Given how fast your temper flares. But I don't." She looked away for a moment and the met Mikoto's gaze, "I suppose I love you too much."

There was a brief moment of silence.

Mikoto just rubbed her forehead, "I am going shopping." She left her crazy friend. She was on the sidewalk, pondering if she should call Uiharu or Saten or simply go by herself.

She noticed a couple fellow Tokiwadai students watching her strangely, keeping their voices hushed. She was about to find out what was wrong when a tall foreigner grabbed her hand.

He was wearing an old fashioned suit, with a large hat on his head. His skin was pale and his eyes were red. In his other hand were a series of bags from Seventh Mist. "Ah, my dear, I must thank you for your advice. I am fairly sure my God-daughter will enjoy these." He leaned over, "Truth is she has fallen for rich playboy type. I keep telling her she will find someone better, but does she listen? No. Kids these days."

Mikoto just said, "Huh?"

Kuroko appeared at Mikoto's side, "Sir? I am a member of Judgment. I have to ask, are you authorized to carry a weapon in Academy City."

The foreigner ignored Kuroko and stared at Mikoto. "I do believe I have the wrong person, only. Your left arm. Have care with it. I recommend you keep it covered."

"Sir I am going to have to insist you back away from my friend."

Mikoto pulled away from the stranger, who was now staring down town. "What are you up to Crowley? Has time come to show you what a true Magician is capable of?"

Kuroko moved Mikoto away from the stranger who kept muttering about magic and other worlds. Both of which were preposterous.

Weren't they?

She looked at her left arm, at the large bruise that was forming. Only it didn't look like a normal bruise. It was too stylized. She shook her head.

The man continued to talk, "No. Rin is here. I must trust in her. Yes. A rougher test than I first thought, but she is tough. I will trust in Rin."

And he was gone.

When Anti-Skill arrived, she answered all their questions. And then had a nice quiet dinner with her friends, all thoughts of shopping put off to another day.

**-End Part-**

A/N- This puts the last of the main characters on the board. The next couple parts they will begin to collide. Hope you folks enjoy.


	4. Chapter 4

A Certain Second Magic part 4

Rin Tohsaka opened her eyes to a strange sight. A girl with red eyes and pure white hair stared down at her. She looked so similar to Ilya, but Rin would place the girl in her late teens. She was over five feet tall and fully developed.

The Ilya she had known had been older than RIn and yet had looked very much like a child.

The girl's eyes opened and she called out, "Dad, she's awake!"

The voice was the same as Ilya's, maybe a slight register lower, but still the same.

Rin shook her head and the world swam. She put a hand to her head and let the world settle. "Where am I?"

The Ilya lookalike smiled and said, "The Emiya residence in Academy City. And If rumors are true you have come from a veeerry long way to get here."

"Do you have any aspirin?"

"Your Circuits are full of mana and AIM." She tossed her head back and smiled, "An easy fix. I'll go get the aspirin though. Tea or coffee?"

Rin took a deep breath, "Coffee."

The girl left to be replaced by a smiling greying adult man. "So, you must be Rin Tohsaka. Old Man Zelretch was talking about dropping you off in a month or so. Then I get a message saying you were in the park. Did he tell you why he sent you here?"

Rin shook her head slowly. "He said something was wrong here. Something not native to this world." She wrinkled her forehead slightly, "A darkness."

Kiritsugu stared at her for a moment, "And that was all?"

Rin sighed, "Yes. He said you would fill me in on the local situation. He didn't even give me time to pack."

Kiritsugu nodded, "That is easily remedied. You are early, but knowing Zelretch you plan or the unexpected. After dinner I will have Ilya take you to some nearby shops to pick up some essentials."

Ilya slipped into the room, "What am I doing after dinner?" She handed Rin a mug and a couple aspirin.

"I need you to take Miss Tohsaka to some of the local stores and…."

"Dad! Can't you have Shirou do it? I had plans this evening with my friends and…."

"And those plans have now changed. One hour shopping will not kill you." He smiled at Ilya, "Normally you would be all over an opportunity to spend my hard earned money shopping. Just last weekend you were complaining about your personal stipend and how it now limits you."

"High school was easier. You didn't charge me rent." She turned to Rin. "So are your parents as rough on you?"

Rin looked at Ilya. The same playfulness was there, but where were the hidden depths? Rin had not gotten along with the tiny woman. The little they coordinated was for Shirou's benift. This Ilya seemed happier, but also more frivolous. "Both of them are dead. All I have is my sister."

Ilya said, "Sorry," and left the room.

Rin looked down. Her thoughts went back to Sakura and all the complications to their relationship. Back to the Grail War and her realization that she was not the perfect Magus she had thought she was. That there were things she would not give up for power. Or even safety. "You did the right thing Mr. Emiya. Fleeing the War…."

"You recognize Ilya. Shirou said you calmed down once you realized who he was. That you muttered his name. Obviously you recognize them. But how?"

"All three of us were Masters in the Fifth Holy Grail War. I was close to your son." She looked away, "He was in love with my sister."

"And Ilya?"

"She was the Einzbern representative. And she was much shorter."

"You know what she is?" Kiritsugu looked away.

"She is your daughter." Family mattered. "Just like Shirou is your son."

Kiritsugu laughed softly, "We will talk about Shirou in a moment. And I find it strange that I would even know the boy." He shook his head, "No Ilya was lucky we came to this city. That I was able to find work here. But then my skills apparently have a universal appeal." He sighed, "It was old world Alchemy verses Academy City super science. There is a doctor called the Heaven Canceller for his miraculous work. He saved her. My beautiful daughter."

"And Irisviel?"

"She didn't make it. She collapsed the portal behind her. What Acht must have done to her….."

"I am sorry. She died during the Fourth Grail War." Rin looked away, "To be honest I didn't even know you. I knew Shirou because we were at the same school."

Ilya peeked back in. "Shirou say dinner will be ready in ten to fifteen minutes."

Kiritsugu said, "Tell him to give me a half hour. Miss Tohsaka and I have things to discuss. Things that will not wait."

She glanced between them, "Right. Call you in a half hour, "And she quickly left.

Rin grabbed the Cross she had made and immediately felt the familiar pain of her Circuits filling with od. She could almost feel the London lab she had made it in. It was just beyond her reach. But she could feel the mana flow into her and flush the foreign mana out.

There were other odd and new sensations she could feel, but now was not the time to indulge in research.

Kiritsugu turned from her, "I want you to tell me everything you know about the Grail War. What you know of the Fourth…. In your world, did I participate?"

"Yes but I am too young to know too many of the details. I know more of the Fifth War."

"So you mentioned. But that war should not have happened until Ilya was old. And yet you say she took part?"

"The Fifth War happened only ten years later, something went wrong and…."

Kiritsugu turned to face her. His face was cold and grim, "Miss Tohsaka, a couple points before we continue. I gave up everything when I came to this world. All to save my daughter. You know she is a homunculus. Despite everything that was done to her, that hasn't changed. Nor has the fact she is the Grail Core. A tiny organ hooked directly to her nervous system that is impossible to remove ensures that.. What she could be used for in this world, I have no clue. But I have no faith in magic users of any sort. No one in Academy City save its governing director know what I or my family are capable of. And you will keep it that way."

Rin swallowed, "I promise."

"Now tell me everything about the grail war and my family's involvement in it."

And she did.

_**Scene Break**_

Mikoto Misaka followed Kuroko up the stairs and into the 177th Division Headquarters for Judgment. "And I am saying you must have imagined it. No one carries a dagger made of gems."

"And how do you explain his disappearance, Sissy? People don't just disappear!"

"So he teleported. You can teleport. What is the big idea?" Mikoto asked. She really had wanted to do some shopping today.

"He was too old to teleport."

"What does that have to do with anything?"

Kuroko ignored her for a moment. "Uiharu? Did you get that footage I asked for?"

Uiharu kept tapping at her computer, a stack of money cards beside her. As always the slight girl seemed happy working at her work station. "I would appreciate a reason so I can log it with Anti-Skill. These cameras aren't for casual use, you know."

"What are the money cards from?" Mikoto asked.

"Someone is abandoning them in out of the way places."

"Why would someone do that?"

Uiharu looked at her and shook her head, "No one knows. And it's not just our district either." Her gaze drifted to her arm. "What happened?" She stood and fetched a first aid kit.

Mikoto tried to wave her off, "No it is only a bruise…"

Uiharu gasped. She glanced at Kuroko and the back at Mikoto. "Why would you do that to yourself? Do you know how hard tattoos are to remove?"

Kuroko looked over, "Cool symbols. Do you know what they mean?"

Mikoto just glared at her friend.

Kuroko sighed, "The Dorm Mother will not be pleased"

"Mikoto looked at her arm and groned.

Kuroko continued, "But at least before she kills you for marking yourself like a common thug, you can bask in the further errors of your ways." She pointed at the screen, "See? A Jeweled sword."

Uiharu let out a whistle, "How expensive is something like that?"

Mikoto stared at the screen, she honestly hadn't seen it. The man had seemed to strange, too eerie. And then like Kuroko said, he vanished.

Uiharu and Kuroko began to argue about the man's teleport.

Mikoto just stood there, a chill washing through her. "What is going on?"

_**Scene Break**_

Shirou Emiya tinkered with the remote drone. He needed something to take his mind off his father's guest. Dinner had been quiet, and she had been appreciative. She had done nothing wrong.

He simply could not forget how she had felt in his arms. Soft in all the right places, firm and strong in others. He had been able to ignore it in the spirit of his run, but the memories lingered.

His mind hadn't been paying attention, but his body had. This was going to be a long couple weeks. Another memory, his watching as Ilya had led her to the bus stop, Rin's hips gently swaying.

He banged his head softly against the right wing of his drone.

He opened the tiny hanger doors and began the preflight checklist.

Everything was green.

He sat at the workstation Ilya had helped him build and launched the drone. The vectored thrust lifted it of just fine, and he flew it through the neighborhood.

On a whim he sent it into the more built up areas of the district. Maybe he could spot some friends, or even his sister. As he passed over he saw movement on a roof. He turned the drone around and reconfigured the wings for slower fight.

He watched as a young woman in a Tokiwadai uniform target a rifle on a target below.

For the first time he regretted not arming the drone.

The girl fired and was almost immediately struck back. His hand hovered over the button to contact Anti-Skill, but hesitated. His father was involved in a great many training exercises. So Shirou contacted him instead.

The drone was now doing tight circles over the building. And he watched the injured girl try to flee. A white haired boy appeared on the roof. He watched the girl try to shoot the white haired boy.

Every attack was reflected back at her.

Shirou was about to contact Anti-Skill anyway, only to have his hand pushed away by his father.

Kiritsugu Emiya's face was cold and grim like Shirou had never seen. "Dad?"

"Have you been recording this?"

"Yes?"

"Erase everything and forget about this."

Both of them witnessed the end of the fight, and the girl's obvious death.

"You can't be serious, Dad." He pointed at the screen, "We just witnessed a murder."

"Listen, Shirou. This City is far from perfect. There are a great many things that I wish I could change. But I can't."

"Dad, we both work with Anti-Skill. We both just witnessed a crime. We can't stop what just happened, but that murdered girl's soul cries for justice and you want me to stand aside." Shirou was gritting his teeth.

Kiritsugu frowned, "Son, if you contacted Anti-Skill right now, the only one who would get in trouble is you. None of the other cameras will show anything. After your gear gets impounded and taken for evidence it won't show what we just saw either." He gripped Shirou by the arms, "These people are good at what they do. They are ruthless and dangerous. You are not ready to face them, not with something as easy to eliminate as your camera's digital file." He stood up, "Sorry Shirou. Remember the good guys don't always win."

Shirou looked back at the screen, "I thought we were the good guys."

"As much as the world lets us. Recall your drone. Wipe its memory. Go to bed." He walked out of the make shift hanger. "Oh and good work on the drone. Polish up the specs and I will submit them for you. Something like that could be useful." And he left.

Shirou gave the recall order to the drone and it flew home, its landing not quite perfect. He erased the onboard computers and work station.

But saved the video file on a flash drive. Everyone deserved justice, even if the gears move slowly.

And Rin wasn't the only think that kept him awake that night.


	5. Chapter 5

A Certain Second Magic part 5

Emiya Shirou was having a series of uncomfortable dreams involving dating Rin while trying to solve a murder. The fact Rin kept flittering between the helpless girl he helped from the park to the self-confident and sarcastic witted woman he had dinner with.

At dinner she had kept giving him mixed signals. Sometimes she had looked at him fondly. And other times like he was a complete stranger. Which he was. For now. But he would very much like to get to know the woman better. Even if she was only going to be a temporary guest.

Assuming there was time. There was so much to repair. And there was his internship in District 23 to consider. Not to mention a few clients he had to meet for his father.

"Shirou. Wake up."

Someone was shaking him.

"Wake up!"

Shirou opened his eyes to see his father in uniform, "Dad? Emergency?"

Kiritsugu rubbed his forehead, "Something like that. Headquarters has something they want me to see. Ilya is home, but Rin is still out there. I need you to find her. I will be too busy and…."

Shirou sat up, "Sure thing." He stretched his arms. He would need the suit. It would let him have an excuse for his abilities.

Plus it was fun.

His father left. Ilya entered briefly after bearing a cup of strong tea. She handed it to him gingerly as if expecting a rebuke.

Shirou asked, "What happened?"

Ilya looked down, "I was actually surprised by here. She is actually kind of cool. She asked me a ton o questions about my life was like. About what being an Esper felt like." She looked up at him, "She laughed when I mentioned all the math involved." Ilya sighed.

Shirou just studied his sister. Out of habit he ran a trace of power through his circuit and cast Structural Analysis. Makeup concealed it from plain sight, but not good old Analysis. "Ryo and his buddies found you."

Ilya straightened her collar a bit, there was a hint of blush in her cheeks, "Just Ryo. Do you think dad…."

"Noticed you had a heavy make out session, I don't know. If you can get those bite marks to heal tonight, maybe. But this is Dad… His ways are inscrutable and all knowing."

Ilya looked down and sighed, "Fine. How do I purchase your silence?"

Shirou stared at his sister, "Did you really dump a complete stranger so you could make-out with your boyfriend.

Ilya shook her head, "Rin is smart. Maybe a little tech dense, but she's not from Academy City, so that's not too surprising. She sort of understood what Ryo meant to me and bowed out. We weren't far and I gave her detailed directions. We got her a phone, but I don't think it will have much of a charge. She hasn't answered anyway."

"Have you tracked the phone's location?"

"You do realize I don't have authority for that? I am not in Judgment anymore."

"Has that stopped you before?" Shirou began to run the pre-diagnostics on the suit. A couple quick taps to the tablet by his bed and it was being prepared.

"Well no, but the risk has to eat into your blackmail. And yes I will provide back up, just hurry. I do need to get some sleep tonight." Ilya left him alone, off to go activate the monster computer she owned.

Ostensibly it was a high powered gaming computer. And Ilya did use it for such. At times. She had learned a great deal working for Judgment, and her Esper power, Thermal Point, allowed her to keep the processors cool no matter how she pushed them. Now she was on the computer security end of the family business.

He got himself suited up an headed into the darkness.

-Scene Break—

Rin had left the two love birds at the restaurant they had stopped at for an unscheduled desert. Watching Ilya flirt with her beau filled her with such conflicting emotions. This Ilya was happy and despite her exotic looks fit in well.

She was happy for the girl, but she brought back memories of the Grail War and all the complications it had brought into her life. And a new taller more alert Shirou….

Not even Rider's strong arms had truly worn away the heartbreak of losing something she had never even had. Save only in a few steamy dreams. Not being able tell him, always supporting Sakura after the War. Honestly, if it hadn't been for Rider providing some stability she might very well have gone insane.

Still as wonderful as Rider was, she lived in Japan while Rin studied in London. And as odd as she found it, no girl could compare to Medusa, so in London she dated guys. Casually of course.

It helped that her apartment was away from the Clock Tower. It cost more, but the privacy was a nice plus.

Trying to clear her mind was why she was out here this late doing martial art moves in the darkened park. Martial Arts had always been part of the Tohsaka tradition, if a part they down-played. It was too bad the most effective techniques did not derive from tradition but from her hated teacher, Kotomine Kirei.

He had been so talented. He had helped with her sister, had helped recover Ilya. And yet he had been thoroughly evil.

Such a waste.

She stopped in the middle of one of exercises. Had she heard something? Like always she had kept part of her mind to pay open to her surroundings. Working with Zelretch had taught her that. He claimed his practical jokes were not just for his cruel amusement, but to teach the need to be observant and mentally flexible.

From her observations, it only made people wary and paranoid. It certainly had that effect on her. She opened her circuits, this time through her amulet. Good sweet prana from London swept into her, bringing its familiar discomfort and pain.

With a thought she powered her Thaumaturgical Crest. It was the fruit of her family's research with spells built directly into the bundle of transferred nerve clusters, allowing her instant access to spells that might otherwise need an aria. Spells like Gandr.

She powered up two, just shy of physically forming. She reinforced her hearing and heard the uneven drone of unpracticed chanting. In badly canted German she heard an aria she never expected.

They were summoning a Servant.

She had to stop this.

A quick reinforcement of her legs and she ran to where the Servant was being summoned. She crested a small hill and saw a hastily constructed Circle made of blood, with several teenagers surrounding it. One of them was wearing a cloak and was botching the spell.

If she hurried, she might be able to stop it before they managed to summon something. So she raised her hand an actualized the Gandr bolts.

Only to have them sparkle and fail. This world did not recognize that spell as cast.

Rin was in trouble, as were the teens. For something formed inside the Circle.

The teens were elated as they saw the creature appear. It was tall, dark, and wearing Gothic style Plate armor. It had a giant sword in its hands.

The summoner approached it, breaching the circle.

And then it killed them.

Rin tried again. She whispered a spell she had read in her father's notes, one that should fire a gout of flame.

Nothing.

And the monster looked up at her and charged.

Discretion being the better part of valor, RIn fled.

_**-Scene Break—**_

Kamijo Touma was happy he had finally finished his homework. The whole scene with the cat had lead him to take Index and Sphinx out to eat, using both time and money he could not afford. It was only when he was making himself comfortable in his tub, when he remembered the Astronomy homework due the next day.

He had even borrowed a telescope from his Teacher, Ms Komoe. The thought of her tears at his failure, let alone what the rest of the class would do to him made him sit up in horror and run out the door, telescope in hand.

He found a nice quiet space and made his observations. It was a bit late, long after curfew, but he was certain that if he were careful, he could get back without trouble.

He should have known better.

First came a thump. He turned to see someone in Anti-Skill power armor glaring at him.

"Shouldn't you be at home? Final curfew was more than an hour ago."

"Well you see…."

A pretty brunette ran past him screaming, "RUN! If you want to live RUN!"

The Anti-Skill officer said, "Rin?"

That is when the monster arrived.

Such misfortune!


	6. Chapter 6

A Certain Second Magic part 6

Mikoto was dreaming deep and dark dreams. A muffled voice in the darkness was trying to give her instructions. A pattern. It was urging her to inscribe a circle on the ground.

In blood.

Any kind of blood, it didn't matter. Animal or human, even stored if that was all she had access to. But fresh human blood worked best.

Mikoto shook her head fiercely. "Never!"

A gentle whispering sigh from the darkness, "So be it child. If not blood then wrought iron or worked silver."

Mikoto smiled. She could fashion one of iron. She called to her the iron sand that now surrounded her and….

"Wake up, dearest sister!"

Mikoto felt a damp cloth placed on her head and a familiar voice from far away call to her. But the iron sand obeys her will and forms a circle full of symbols on the ground before her.

The voice from the darkness snickered and said, "So risky to summon anything with your only protection able to be blown away." A wind kicks up and tries to disturb the sand.

But Mikoto's will was stronger. She maintained the circle. But the voice was also right. So she used another potion of her power and fused the sand together.

"Please wake up, Sissy. You will wake the Dorm mother and, and…."

Distantly she felt a weight on her body. Something told her she was vulnerable. That she needed to wake. Then she heard a feminine giggle, and she began the long trip from the darkness back to the real world.

The voice cried out, "No, you need the Aria. The Circle alone isn't enough!"

"I guess only a kiss will bring my beloved Sissy back."

Mikoto felt a soft pressure on her lips as she woke. She pushed Kuroko back and lashed out with a bolt of electricity. "Get off me. We have talked about this… before?" She looked at the room. All the lights were on. In fact all of the electrical appliances were on. Saint Elmo's Fire air rippled along every pointed object in the room, which hissed and popped. A couple of bright balls of light danced in the air.

Air that tasted heavily of ozone.

Above her belly there was a spinning black circle. Intricate in detail, it was still cooling, nestled in a cradle of magnetic fields. Mikoto did not want to touch it, so she slid out of bed underneath if. When her foot hit the floor, she felt a hand grab her foot.

And she was suddenly on the dorm roof, Kuroko gasping next to her. "Eh, if we get caught…."

Kuroko sat up and glared at her, "Bad dreams, Sissy?"

Mikoto looked away, "Strange ones." She tried to remember, there was something she needed to know that she didn't. She muttered, "I won't be able to summon it yet."

Kuroko was now looking at her alarmed, "Summon? What are you talking about?"

Mikoto looked over at her friend, "Eh? I am not quite awake yet."

Kuroko sighed, "I have never seen you like this before. You occasionally arc a little bit, but nothing like tonight."

Mikoto said, "Wait…. You watch me while I am sleeping?"

Kuroko smiled at her, "Sometimes. When I can't sleep. I don't crowd you, I don't touch. I respect your privacy." Her smile widened, "It is just you are so cute when you sleep. And then you…. " Kuroko was quiet, "You are going to hurt me again, aren't you."

Mikoto held back a bolt of cleansing electrical current. It wouldn't solve anything, and it might get them caught. "Maybe. It is just a little creepy. What would you do if I started watching you in your sleep, or was hovering over your bed staring at you?"

Kuroko thought for a moment, "Come lay beside me, my love. The bed is narrow, but there is room for two."

Mikoto stared at her friend. "Did you actually just say that?"

Kuroko shook herself proudly, "Not ashamed of it at all. Although if you are going to fry me, can you wait until we are in our room? The last thing we need is the Dorm Mother on us as well."

Mikoto sighed and looked down, "I am too tired to fry you." She looked back at her friend, her cheeks red, "You do know that while I like you, I don't, you know."

Kuroko smirked, "Like you like that? Is that what you were going to say? Honestly Sissy, you are such a child at times. What are we in, Grade School? I know you don't care for me like I do you. At least not yet."

"I think you are in for a long wait, Kuroko."

Kuroko nodded, "Maybe so, but you are worth the wait. Come let us go back to our room." She grabbed hold of one of Mikoto's arms and they were in their room. Kuroko looked furtively around it, checking the bathroom.

Mikoto was drawn to her bed. There was a little bit of smoke coming from a singed set of sheets. There resting in the center was cast iron circle around ten centimeters across.

The detail on it was intricate. It was nearly identical to the Circle she had seen in her dreams. She couldn't remember anything else, but the Circle was very real. She picked it up, it was still warm but not hot.

Kuroko walked around to take a look at it. She said in an offhand manner, "Now is the time to fry me if you are going to. I regret nothing." She looked over at Mikoto. "Sissy?"

Mikoto waved the Circle around, "This means something to me, Kuroko. But I have no idea what."

Kuroko yawned, "Well, I suppose I can have Uiharu look it up tomorrow." She grinned suddenly, "Or maybe Saten will know about it. It looks like something she would be interested in."

"Huh?"

"You know how she is always going on about those wacky superstitions."

"Yeah. Look, I don't think I can sleep for a while. But don't let me hold you up."

Kuroko waved her hand, "That is okay. I would keep you company if you wish. Tell you boring stories about some of my teachers. They almost put me to sleep when I am there, and you know how seriously I take school."

And so they talked deep into the night.

_**Scene Break**_

Touma ran next to the man in armor. He was tempted to stop and see if Imagine Breaker would work on the monster behind him, but just once he wanted someone else to do the heavy lifting.

And then he tripped on a rock.

"Such misfortune."

A loud cry as the monster saw him. Touma turned and placed his right hand in front, which hopefully would stop whatever it planned on doing to him.

The man in power armor was back and he rammed into the monster knight. "Run, kid." For a moment it looked like he might subdue the monster, until it knocked him off and swung its oversized sword. The man and his armor went flying.

The monster knight now focused on the guy in power armor. Surely Academy City's finest could deal with a monster. Surely it was fine for him to go. So he dusted himself off and prepared to leave.

But the man in powered armor wasn't winning. He was getting battered around the clearing, occasionally getting in a shot, but mostly acting like a target.

And then the girl returned. He could sense she had a power about her, but it was unfamiliar. One of her hands was cut and the blood was pooling into the other hand. And she was muttering in a foreign language.

The knight positioned the powered armored man in such a way as he could not dodge. He brought up the sword to kill, and that Is when the night exploded.

The girl proclaimed loudly:

_**By my blood, and for my blood,**_

_**Bring forth pain and misfortune unto my enemy**_

_**Through my blood!**_

The girl threw the cupped blood and with bright blue and red and green fire, long jagged crystals of blood shot forth at the monster knight. They dug deep into the knight's armor and it howled in agony.

It then turned and screamed its hate at the girl and began to run at her.

The girl just stood there, pooling more blood into her hands. In the moon light she looked like a goddess bathed in red and black and white. She raised her hands once more.

_**Power calls to power**_

_**And blood calls to blood.**_

_**I place my power into my blood,**_

_**To kill the one I hate!**_

This time there was a flash of crimson lighting that stretched to the charging knight. It did not slow him at all.

The girl just stood there, confident and calm.

He had to help her! He began to run, fearing he would be much too late.

And in a sense he was. Somehow the man in powered armor was not only alive but moving quickly.

Very quickly.

In a way it was a surprisingly fortunate thing for Touma. For the armored man got to the knight not only before it got to the girl, but also before it exploded.

_**Blood of my blood, that which dwelt within my heart,**_

_**A heart that seethes and burns with hate**_

_**For this monster summoned from the depths of time and space.**_

_**I ask you to take up this burden of hate from your former home,**_

_**And explode upon mine enemy!**_

Every drop of the girl's blood turned into a tiny bomb. Every speck and crystal of it inside and on the top of the knights armor exploded in a wash of crimson light.

Reflexively Touma shielded himself with his right hand.

The girl was relatively unharmed, although she was breathing heavily. She was searching for something, "Damn you Emiya, I won't let you die on me again."

Touma saw the knight and the powered armored man and he called out, "Over here. Both of them are over here."

The powered armor looked intact, the ancient knight did not. There were more holes to the armor than there was armor. There was no body inside.

Touma sighed. Of course not.

Had his life always been this insane before he lost his memories?

The girl quickly made her way over to where the man in powered armor lay. She fiddled with the helmet for a moment before removing it. "Oh, thank God you are alive!"

The man said weakly, "Rin?"

She smacked him. Hard.

Touma could only wince. It was nice not to be on the receiving end of it for once though. He should leave now, while they were distracted.

Just to be certain he walked over to the knight and touched him with his right hand. And was rewarded by a trail of glowing gold as the armor evaporated.

It was time he left. And so he did.

_**End Scene**_

Shirou gasped as Rin slapped him. "What was that for?"

Rin just remained above him, shaking slightly. "You could have been killed."

"I was just doing my job."

"Right because fighting supernatural monsters is a part of Anti-Skills job set."

Shirou knew he would pay for it, but he smiled anyway. "You might be surprised."

She grabbed him by shoulders of his armor and began shaking him, "Why do you always do this! You always throw yourself into danger never caring about the consequences. One of these days it is going to get you killed! And then where will Sakura be! Where will I…." She looked away.

Shirou said softly, "I am not your Emiya. Not your Shirou. I do like you. But I am not him."

"I know that. I do."

"Then don't treat me like him."

"Okay," She said softly.

Shirou reached up and wiped away some tears, "I don't deserve these. Not yet."

She nodded, but the tears continued to roll down her cheeks. "My Shirou died. I never got to tell him that I liked him, that he was right. That killing Sakura was wrong. That we needed to find another way. I really would have done it at the Church. I would have, but you stopped me. I would never have forgiven myself. You pushed yourself and pushed yourself until you died. And you saved us all."

"I am not him."

Her eyes lit up and anger poured off of her, "But just now you were acting just like him. Throwing yourself at the monster. Don't you have guns or something? Any kind of weapon? Did you have to try to wrestle with a sword wielding Wraith?"

"Just the non-lethal stuff I always carry. I was looking for you."

RIn sighed, "I just needed some space. I probably should have told someone, but you were all so busy. I didn't want to bother you."

"Next time, at least carry your phone. You obviously can take care of yourself."

Rin just nodded.

"Hey, where did that kid go?"

"Don't worry about him. I am more concerned about the Circle in the center of this park."

Shirou sat up, "I should go report that."

"Mind if I join you? I know you aren't my Shirou, but I do like you." She stood up and was carefully not looking at him, "I mean, I am only here for a short time. And I would like to get to know you better."

Shirou smiled at her, "If it will make you happy, sure."

Rin winced a little at that and handed him his helmet. "Let's go hero."

And Shirou reported the Circle. It was the fourth reported that night. Supposedly some monster was still prowling in District Ten. But with all the damaged cameras no one could quite track it. A couple of Anti Skill Crash teams were ready if there was word.

For many it was a tense night. But for Shirou and Rin it wasn't so bad. After finishing up the paperwork from the crime scene, both of them spent time talking until long after the sun rose.

_**End Scene**_

Ilya stayed up late into the night as well. At first it was the fun of hacking into the system, seeing what loopholes had been fixed. And what vulnerabilities remained.

Some people really did not have a security conscious mind. Or imagination regarding passwords.

But after finding Rin's phone on the dresser of Rin's room charging…. She definitely felt like she was on a wild goose chase. In retaliation she raided his warehouse looking for suitable blackmail material of her own.

She knew from the friends she had set up dates for him with, that her brother was fairly clueless. Most of them ended up being friends of his as he fixed some appliance or vehicle of theirs. Or cooked dinner.

A friend of hers once confided in her after breaking up with Shirou, that he was nice, but empty. That he derived pleasure solely from helping others. And while that was nice, he would never let her reciprocate unless he was certain it would make her happy. He simply didn't care about his own happiness.

And looking back on her childhood, from when he had joined them, Ilya could say that was true.

Still, no one was perfect. He had to have some dirt here somewhere. He was always sending that drone out. Perfect time for spying on cute girls. Ilya smirked. She took out the most recent disc.

Empty.

Ilya nodded to herself. There had to be something here. Maybe her brother was human after all.

She checked the on board memory. It had been wiped as well. But then Shirou was conscientious about his equipment. He probably wiped it so it would be ready for tomorrow.

But where were the backup discs. Ilya had been an Emiya her whole life through, and one thing she knew was that you never completely destroyed a source of information. You never knew when it might come in handy. You always store a backup. And a backup to the backup.

Ilya used her vast knowledge of Shirou to divine where he squirreled it away. Pretty slick too, no one, not even Dad would check among these discs.

Ilya danced her way back to her room and her computer and played the disc. It started normal and dull, like all his flights. She almost stopped it running, certain nothing would be here. But a little itch told her to keep watching. That something had happened.

She watched as a sniper took aim and fired, only to get shot back at. She watched as the sniper tried to run and was caught and killed.

Only there were a couple of details that Shirou probably missed. One the girl was wearing a Tokiwadai uniform. Two, the girl was famous. Or was imitating the famous Railgun of Tokiwadai.

Of course the Railgun didn't need a sniper rifle to show her displeasure.

And the killer seemed familiar somehow. She couldn't quite place the face, but she would after a quick analysis.

This was golden blackmail material. Her brother was covering for a murder.

Ilya placed a finger on her lip. Shirou didn't work that way. He was Anti-Skill through and through. He would have reported it. At least to Dad if to no one else.

A chill ran down her spine. She nodded to herself. That is what must have happened. Only Dad told him to erase the tapes. This wasn't blackmail material at all. Or rather it was, but on her father.

And while she loved him dearly, would live or die for him in a heartbeat, she was still afraid of him. Not the normal playful father he normal showed to the world. But the cold blooded killer that he could be if pushed.

While Anti-Skill did not officially have a Black Ops division, its head, assuming it actually existed was Kiritsugu Emiya. That didn't mean there weren't other groups out there, some with Esper support, some without. Her time in Judgment had jaded her more than a little, as she watched some of what was going on. And with her contacts in Anti-Skill through her father, she knew that Academy City had a dark side it tried to keep hidden.

She also knew it was part of the whole, and that containing it was much more reasonable than trying to purge it.

Explain that to Shirou, however. He would never see it.

What she should do is purge the data on her computer and damage the disc so it would lose its ability to store media. She could do it and Shirou would probably never know. Rapidly oscillating temperatures was bad for most materials.

But at the same time…. Someone had died. She might not believe in the purity of Justice like Shirou did, but….

Ilya had been offered large sums to join some of the darker outfits out there. Scientific Outfits that weren't just pushing the margins but breaking them. Sometimes for her computer skill, sometimes for her Esper power, often for both.

She had stayed on with Emiya Research Associates, not just out of family loyalty. She stayed because while Shirou's outlook was so flawed it wasn't funny, it would be nice to imagine that the world might become better than it was.

Ilya closed her eyes, "This is so stupid."

She put the disc back for Shirou to find. She also had a copy hidden in the files of her computer, and her backups carefully hidden.

She finished up a little homework she had and instead of going to sleep she began to run the killer's picture through some filters to find his name.

A couple hours later she woke to find her program had found its target.

The computer was 98 percent sure that the killer was Accelerator.

Ilya shut down the system and checked. No one was home. She shivered. Usually she liked the silence, the privacy.

Not at the moment.

She almost didn't take a shower because that was where the killers in movies always killed the pretty girls. And her mind kept seeing the poor girl's broken body. Where Accelerator had merely TOUCHED her. Ilya shook.

It was a long and sleepless night for Ilya Emiya.


	7. Chapter 7

A Certain Second Magic part 7

Mikoto Misaka sighed as Kuroko lead her into the hospital wing. "Seriously, I don't need this."

Kuroko looked at her sideways, "First we find out about that bruise you have. You say you didn't get a tattoo, but there one is on your arm. If we can come up with a medical reason it is there, the Dorm Mother will not kill you."

"I told you…."

Kuroko raise a hand, "Second, you woke me a second time, after we had spent hours talking, with another ridiculous display of power in our room. All the while muttering that you were all the good in the eternal world, and that you were the disposer of evil in the eternal world." She shook her head, "There was more, but you kept repeating that phrase. Seriously, Sissy, something is wrong."

Mikoto looked over at her friend, "I am fine." Truthfully she didn't feel fine. Her head was aching and she could use a few more hours of uninterrupted sleep. And she felt vulnerable and on edge.

"Honestly, Sissy. Why do you always have to be so stubborn? If I or any of our friends were acting half as oddly you would be bundling us off to the hospital just like this. Is it so hard to accept help from us? Have I not been at your side when you needed me?"

"Kuroko…"

The next part was never fun. Paperwork. Even a technological city like Academy City seemed to thrive on it.

Then came a battery of tests, all of which needed to be calibrated to her ability. One of the reasons she hated being in a hospital was how the nurses would always groan when they found out she was an electromaster.

Mikoto Misaka was after all a walking talking source of unshielded electromagnetic radiation. Her mere presence could throw off sensitive equipment. Fortunately electromasters were common enough that a workaround to the problem had already been thought of. It required calibration to the level of radiation emission, which with Mikoto was large enough that she could use it as a pseudo radar….

She was surprised by whom Kuroko was quietly chatting with. As far as she knew Doctor Kirama was still recovering from her long and successful crusade to save her students. Students she would be teaching at the same school Uiharu and Saten went to. The Doctor looked healthy and rested. But that didn't explain why she was here.

Or why Kuroko seemed worried, a worry that did not fade when she looked up and saw Mikoto. "Sit down Sissy. You need to hear this."

Mikoto nodded slightly to Doctor Harumi, "It is nice to meet you. I am a little surprised. I thought you were still recovering."

She nodded, "I am on light duties. But today was hectic enough that they are letting me help. Honestly I was going crazy sitting there simply resting." Her smile was slight, "I am afraid I have become a workaholic."

Kuroko shook her head, "Please, Doctor Harumi, tell Sissy what you told me."

She looked at Kuroko with a confused expression, "About the potential dangers of the Personal Development curriculum? I have already told her."

Mikoto stared at her, "Huh?"

"That aspects of the Personal Development Project are not entirely safe."

Mikoto looked away, "Well she did. But I didn't think much of it at the time."

Kuroko stood and waved her hands emphatically at Mikoto, "Sissy, she says we might all go insane!"

Doctor Kiyama sighed and sat back in her chair, "Sit down Kuroko. I didn't say that. I did say there is a high correlation with increased levels of insanity among the higher level espers."

"You said Sissy was the only sane Level Five!" Kuroko shouted back.

Mikoto noticed others in the hallway were looking over at them, but she had to know…. "What?"

Dr. Kiyama looked at Mikoto, "Is she always this excitable? She seemed levelheaded the last few times we met."

Mikoto glanced over at Kuroko who was glaring at Dr. Kiyama. "Well…."

Kuroko shot her a glance and then took a deep breath. "I am sorry, this just struck a nerve. One of my friends is always saying that I am crazy."

Mikoto forced a smile, "Uiharu doesn't really mean that, Kuroko."

Kuroko shot her a glare.

Mikoto said softly, "Much."

Kuroko switched her glare to Dr. Kiyama, "So were you pulling my leg when you said I needed to protect Sissy's sanity?"

Dr. Kiyama looked sheepishly over at Mikoto, "No. I would very much like you to do that. While correlation is not causation, every other Level Five is insane."

Mikoto just stared at her, "What?"

Kiyama calmly reached over to a coffee cup nearby and took a sip. "Come with me, we are making more of a scene than I anticipated. It is perhaps better to do this in private." She stood up and began walking.

Mikoto followed, as did Kuroko. Kuroko was grumbling and visibly unhappy about it. Mikoto quietly asked, "What did she tell you?"

Kuroko shook her head, not in her usual aristocratic fashion, but a simple worried movement, "Too much maybe, and yet not enough." She looked a little sheepish, "I did tell her about your dreams last night. I mean she is an expert in neurology, right? She might know what caused it."

"Kuroko…. That was private! How could you tell someone about last night?"

"You scared me, Sissy. The second time last night was worse, much worse than the first. Only this time it was restrained." She laughed quietly for a second, "Funny how that was more frightening, but it was. Because it meant that something was controlling the display, you were controlling it while you were sleeping." She paused a moment and looked seriously at Mikoto, "I am not a Level Five, and while I want to be one, I know I have a long way to go." She looked away, "But there is more to my ability than just spatial movement. To do what I do requires a feel for the fabric of space and time, to be able to use those complicated eleven dimensional vector transformations requires that sensitivity." She looked over at her friend, "It also requires a feel for energy transformation. When I teleport up, everything I move, including myself has to have energy added to it to counter the energy lost due to increased potential energy. To teleport down, the reverse." She shook her head grimly, "I have a feel for these things Sissy, I have to."

"Kuroko…."

"Let me finish, Sissy. Last night our room was filled with so much energy I do not know how we didn't turn to cinders. I could see the magnetic fields you were creating, they were laced with plasma." She shook her head, "That was beautiful by the way." She took a deep breath, "The room was lit as if it were noon, little balls of lightning roaming around the room. Arcs flashing and sparking all through the empty spaces. But nothing was set on fire. Nothing was damaged. Fogs of concealing iron sand walled off the windows and the door. It was like our conversation did nothing but insure you would not wake the Dorm Supervisor."

Mikoto looked away, "I am… sorry Kuroko. If you… want to change rooms. If, if you are frightened of me now, I would understand." Mikoto felt the hands of her friend grasp her shoulders and shake her slightly. She glanced at her friend.

Kuroko had a tear in her eyes, but she was smiling, "Stupid stubborn Sissy. I am not scared of you, I am scared for you. Throughout all of that display, I was untouched. Even when I walked over to your bed, the energy waves and magnetic fields moved to avoid me." She hugged her, "You are my best friend."

Mikoto returned the hug. A moment later she tried to pull away.

Kuroko clung to her and held tight.

"Kuroko…."

"Just a moment more," Kuroko sighed. "Remember you are in a hospital. You don't want to damage any sensitive equipment."

Dr. Kiyama called back, "Are you two coming?"

"Kuroko…."

"Just a moment more."

Mikoto closed her eyes and sighed, "You leave me no choice." She maneuvered herself slightly to get a better grip on her clingy friend.

And broke Kuroko's hold and landed a solid blow to her head. "Limits Kuroko. There are limits."

Kuroko rubbed her head, "I know Sissy, I just was enjoying the moment."

Mikoto sighed, "Let's go hear the rest of what Dr. Kiyama has to say."

_**Scene Break**_

Ilya sighed as her mother tucked her into her bed. "Tell me a story, Mommy!" Her voice was high and childish.

(Wait. Could I even talk when Mom was still alive?)

Irisviel was beautiful and graceful as moved about the room, her gaze always coming back to Ilya. "I didn't mean for this to happen. I never expected there would be a way that I could see you again. That I could see," She closed her eyes. "How is Kiritsugu? How does my husband fare in this new world?"

"Papa Kiritsugu is an important man! He works for Anti-Skill and, and he runs his own consulting company!" Ilya said bouncing on the bed, her tiny body barely making an impact on the covers.

(Yeah and I am in charge of computer security for said company. Why am I such a kid? And why am I so tiny?)

Irisviel plucked her from her bed and held her, dancing around the room. "I love you my sweet. You must be strong my darling. I am not alone here, this is my wish, my desire, but I am not alone." Irisviel held her close, "She is here, always only half awake, stuck in her ways, still reaching out and calling." Irisviel shuddered, "And HE is here. You must fight HIM, my lovely Ilyasviel. You must fight him will all that you are, and all that you have become in your new world."

"Momma?" (What is going on here? Why did you leave us? Did I do something wrong? I promise I will fix it! I promise to be good. Just, just come back to us.)

"I must go."

(No! Don't leave me! I love you. I will do anything, ANYTHING! Just don't LEAVE ME!) "Momma, is something wrong?"

"I didn't want this for you my sweet. I gave up everything so you would be safe. And still I failed." Irisviel's face was covering tears and regret, "I just wanted to see you once more. One tiny little wish." She pulled Ilya even tighter to her, "Why is the universe so unfair? Why…."

And she was gone.

_**Scene break**_

Ilya shot up in her bed. More than any dream of Accelerator breaking her body, that dream haunted her. It had been years since she had dreamed of her mother.

Ilya shook her head and got out of bed. The night full of nightmares and odd dreams had left her sweaty and gross, and she needed a shower before she could face anyone.

Luckily she had her own bathroom. While space was at a premium in the district they were in, her father had money and influence. And so while they were not located in one of the truly wealthy districts, her house was really kind of nice.

Of course, her father being Kiritsugu Emiya, that meant more in the way of pragmatic creature comforts rather anything fancy or elaborate. It looked nice, and one of the guest rooms was really fancy. But most were simply comfortable and convenient.

Ilya was just happy to have her own personal bathroom. She spent a few minutes debating on whether to take a bath or not, before deciding to just take a shower. She was hungry after all.

As she washed her hair and cleaned her body, her mind started to become strange. She stopped the shower for a moment to clear her head. And got out of the shower.

She looked at herself in the mirror. Her hair was a gleaming silver white, and her eyes a brilliant red. And along her belly a series of complicated sigils formed. Each made of three complicated brush strokes.

'Those must be the Command Spells.' Ilya thought idly, her mind strangely serene. 'It must be time.'

She walked out of the bathroom, not bothering with a towel.

She wouldn't need it anyway.

She climbed onto the Altar that had replaced her bed, laying calmly down on the hard marble.

Ilya took a deep breath. And she said to the empty air, "I am ready."

(What? I, I thought I was awake. I thought, I thought…. No, this isn't real. I don't accept this. Wake Ilya, wake up!)

The Ilya on the Altar caught on fire. Ilya could feel as the flames consumed her unresisting body, feel as the flesh was burned away.

Leaving only a Golden Chalice behind.

A deep voice echoed throughout the chamber, "_**Accept your FATE, child. You ARE the Holy Grail….**_"

Ilya woke up screaming.

In seconds Shirou was there holding her. "I am here, Ilya. You are safe."

Ilya looked up at him, tears streaming down her face, "Can you protect me from myself? Can you protect me from Fate!"

Shirou looked deep into her eyes, and with complete conviction, "You are my sister, Ilya. I will do anything to protect you. Anything."

Ilya closed her eyes and clung to her brother. Because he really would do anything to protect her.

Shirou continued, "You and Dad, you took me in when I had nothing. When I was nothing. I would give up my life for either of you in a heart beat."

Ilya opened her eyes, a wry smile amidst the tears, "And little Miss Rin Tohsaka?"

"What? I don't know what you are talking about."

Ilya giggled slightly, feeling safe in her brother's arms, "You were out with her all night. The door camera's didn't see you entering until a little past nine. AM. So…."

Shirou just sighed, "I like her, Ilya. Is that wrong?"

"Not at all. But if you like her, just remember she won't be here for long. And if she is like Zelretch, she will always be travelling."

"So you don't think it is a good idea?"

Ilya laughed, "No, brother dear, go for it. Don't waste time. I will help you as I can."

"Ilya…."

"Nothing underhanded, I assure you."

"But my happiness isn't…"

She put a hand over his mouth, "your happiness is important to me, Shirou. How can I be happy when you are not? And trust me, you are much more pleasant to be around when you are getting some than when you are not. If only you weren't so obsessive about your stupid machines…." She shook her head, "If Rin makes you happy, and you accept that she will only be here for a short time, go for it. And maybe, if you actually manage to fall in love for once, I can understand what makes her different. And find someone who can hold on to you for real."

"Ilya…."

She just smiled up at him. "Shirou?"

He just shook his head, "Are you better now?"

"Mostly. Thanks. Did Dad ever come home?"

"No. Besides, he would have beaten me here."

"Hmm, well I am going to take a shower." She looked up at him and smiled, "You know what would really make me better?"

He looked at her suspiciously, "What?"

"Pancakes."

"Pancakes? Ilya it is three in the afternoon."

"So? I just woke up. That means it is time for breakfast. And I want pancakes."

Shirou backed away, "If that will be all Your Highness?"

"Yeah, no wait. One more thing. A favor. Can I borrow the Nightwing tonight?"

Shirou looked confused but nodded, "I do have an appointment this evening. Okay. Just promise me you will do all the preflight checks. Oh, and save all the data, I would like to look it over. I don't necessarily care for what the footage of the camera shows, but the stability data and electromagnetic sensors are important for Dad's releasing of the designs to Anti-Skill."

"Whoa, are they going to buy the design?"

Shirou shrugged, "He said they would look at it. I have already submitted the patent information to Administration. If it is approved they will log it with the various National and International Patent organizations."

Ilya squealed and leapt on her brother, "I am so happy for you! And jealous. But mostly happy."

Shirou shrugged, "Just because I have a patent means nothing, not unless someone uses it. Legally. But my first royalty check, I will treat you to dinner. How does that sound."

Ilya nodded. "I need to take a shower, and you need to make some pancakes."

Shirou gave her a kiss on the forehead and left, closing the door behind him.

Ilya stared at the door for a moment, the fear returning. She took a deep breath and walked into her bathroom, discarding her pajamas as she went. She took a quick shower and dried herself off quickly.

There were pancakes with her name on them being made that very moment. She could smell them.

She stopped and glared at the mirror, daring it to all be a dream again.

Ilya addressed the open air, "I don't know who you think you are fucking with, but I am Ilyasviel Emiya, and I am my father's daughter." Her eyes tightened, "And if you keep screwing with me, you will understand what that means to your ETERNAL sorrow."

Nothing happened.

She grimly left the bathroom and quickly got dressed. She would be home all day, so she dressed casually and comfortably.

She paused again.

Still nothing.

"I will be watching for you. I won't be surprised a second time." Ilya called out. She took a deep breath and with one last glare for her room, she left. A smile sliding into place.

She was hungry, and Shirou was a good cook. And he was making her pancakes.

The mystery could wait.

_**End Part.**_

A/N- Hopefully the next part comes faster than this, but sadly life has the right of way. The next part should have Shirou and Mikoto meeting, and Ilya and Rin playing with the Nightwing drone of Shirou's. Plus a little bit of what poor Touma is going through.

Thanks for the reviews. Until next time.


End file.
